Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= reanno::Smeli:SMc03062 (336 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 123 bits (309), Expect = 5e-33 Identities = 78/243 (32%), Positives = 127/243 (52%), Gaps = 16/243 (6%) Query: 49 IANSIRPWLFLAPALLALTLYLVYPVVQSVWLSL-----HGRGGQNFVGLSNYSWMINDG 103 + + + P+LFLAPAL L L + +P +Q+ + S + +VGL N+ ++ND Sbjct: 4 LRDRLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDA 63 Query: 104 EFRQSIFNNFLWLLVVPALSTFFGLIIAALTDRIWWG-NIAKTLIFMPMAISFVGAAVIW 162 F +++ N F++L+ V L F L +A L +R G + + + P+ +S V A + W Sbjct: 64 VFWKTLGNTFIYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAGIAW 123 Query: 163 KFIYDYRAAGSEQIGLLNAI---VVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVI 219 +++Y + GLLN + V G +P W+T P F +M + +W G+ MVI Sbjct: 124 RWLY-------AETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVI 176 Query: 220 LSAALRGIPEETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAM 279 A L+GIP E EAA +DG++GW+ I +P + + +V I KVF+ V M Sbjct: 177 YLAGLQGIPLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIM 236 Query: 280 TNG 282 T G Sbjct: 237 TQG 239 Lambda K H 0.330 0.142 0.466 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 261 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 336 Length of database: 293 Length adjustment: 27 Effective length of query: 309 Effective length of database: 266 Effective search space: 82194 Effective search space used: 82194 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory